Multidimensional Genome - Dr. Robert Carter


Uploaded on August 04, 2012 by TheWordisalive

Skittle: A 2-Dimensional Genome Visualization Tool - Josiah D Seaman and John C Sanford

Mathematicians find that microRNA performs many actions 'simultaneously' to the protein development, basically acting to get the job done (regulating the speed of protein production) in a stable and efficient way, given whatever conditions the experiment is occurring in.

Mathematicians find solution to biological building block puzzle - July 31, 2012
Excerpt: For a long time molecular biologists thought that the major role of RNA in living cells was to serve as a copy of a gene and a template for producing proteins, major cell building blocks. This belief had been changed at the end of 90s when it was found that myriads of RNA molecules are involved in regulating speeds of practically all molecular mechanisms in a cell. These abundant molecules are essential in regulating the speed of protein production– a vital function in bodily processes, including development, differentiation and cancer. The problem to date has been that scientists have differed over interpretations of how the production of the major building blocks of a cell, proteins, is controlled by microRNAs. Basically, there were different and sometimes conflicting theories about ways in which microRNAs regulate protein production since the results varied depending on only slightly changed experimental conditions. ,,,
"Quite dramatically, there has been a series of reports in top-ranked journals with contradictory results supporting one or another mechanism. Furthermore, researchers are puzzled by the fact that the same couple of protein and microRNA demonstrate different mechanisms of regulation in different biological labs or in slightly changed experimental conditions.",,,
Professor Gorban said: "We have shown that what appeared to be very different mechanisms are in fact manifestations of one relatively simple biochemical reaction, but taking place in various contexts. "Our model proposes that microRNA performs many actions simultaneously to the protein development, basically acting to get the job done (regulating the speed of protein production) in a stable and efficient way, given whatever conditions the experiment is occurring in.

The Extreme Complexity Of Genes - Dr. Raymond G. Bohlin - video

Astonishing DNA complexity demolishes neo-Darwinism - Alex Williams
Excerpt: Not only has the ENCODE project elevated UTRs out of the ‘junk’ category, but it now appears that they are far more active than the translated regions (the genes), as measured by the number of DNA bases appearing in RNA transcripts. Genic regions are transcribed on average in five different overlapping and interleaved ways, while UTRs are transcribed on average in seven different overlapping and interleaved ways. Since there are about 33 times as many bases in UTRs than in genic regions, that makes the ‘junk’ about 50 times more active than the genes.

This following study, that discovered a 'Second Regulatory Code" on top of the protein coding DNA code, should have, by all reasonable accounts, completely stopped the neo-Darwinian claim for 'Junk DNA' dead in its tracks:

Nature Reports Discovery of “Second Genetic Code” (Splicing Code) But Misses Intelligent Design Implications - May 2010
Excerpt: Rebutting those who claim that much of our genome is useless, the article reports that "95% of the human genome is alternatively spliced, and that changes in this process accompany many diseases." ,,,, the complexity of this "splicing code" is mind-boggling:,,, A summary of this article also titled “Breaking the Second Genetic Code” in the print edition of Nature summarized this research thusly: “At face value, it all sounds simple: DNA makes RNA, which then makes protein. But the reality is much more complex.,,, So what we’re finding in biology are:

# “beautiful” genetic codes that use a biochemical language;
# Deeper layers of codes within codes showing an “expanding realm of complexity”;
# Information processing systems that are far more complex than previously thought (and we already knew they were complex), including “the appearance of features deeper into introns than previously appreciated”

Researchers Crack 'Splicing Code,' Solve a Mystery Underlying Biological Complexity - May 2010
Excerpt: "Understanding a complex biological system is like understanding a complex electronic circuit. Our team 'reverse-engineered' the splicing code using large-scale experimental data generated by the group,"

The data compression of some stretches of human DNA is estimated to be up to 12 codes thick (12 different ways of DNA transcription) (Trifonov, 1989). (This is well beyond the complexity of any computer code ever written by man). John Sanford - Genetic Entropy

The multiple codes of nucleotide sequences. Trifonov EN. - 1989
Excerpt: Nucleotide sequences carry genetic information of many different kinds, not just instructions for protein synthesis (triplet code).

John Sanford, a leading expert in Genetics, comments on some of the stunning poly-functional complexity found in the genome:

"There is abundant evidence that most DNA sequences are poly-functional, and therefore are poly-constrained. This fact has been extensively demonstrated by Trifonov (1989). For example, most human coding sequences encode for two different RNAs, read in opposite directions i.e. Both DNA strands are transcribed ( Yelin et al., 2003). Some sequences encode for different proteins depending on where translation is initiated and where the reading frame begins (i.e. read-through proteins). Some sequences encode for different proteins based upon alternate mRNA splicing. Some sequences serve simultaneously for protein-encoding and also serve as internal transcriptional promoters. Some sequences encode for both a protein coding, and a protein-binding region. Alu elements and origins-of-replication can be found within functional promoters and within exons. Basically all DNA sequences are constrained by isochore requirements (regional GC content), “word” content (species-specific profiles of di-, tri-, and tetra-nucleotide frequencies), and nucleosome binding sites (i.e. All DNA must condense). Selective condensation is clearly implicated in gene regulation, and selective nucleosome binding is controlled by specific DNA sequence patterns - which must permeate the entire genome. Lastly, probably all sequences do what they do, even as they also affect general spacing and DNA-folding/architecture - which is clearly sequence dependent. To explain the incredible amount of information which must somehow be packed into the genome (given that extreme complexity of life), we really have to assume that there are even higher levels of organization and information encrypted within the genome. For example, there is another whole level of organization at the epigenetic level (Gibbs 2003). There also appears to be extensive sequence dependent three-dimensional organization within chromosomes and the whole nucleus (Manuelides, 1990; Gardiner, 1995; Flam, 1994). Trifonov (1989), has shown that probably all DNA sequences in the genome encrypt multiple “codes” (up to 12 codes).
Dr. John Sanford; Genetic Entropy 2005

DNA - Replication, Wrapping & Mitosis - video (notes in description)

In Embryo Development, Non-DNA Information Is at Least as Important as DNA - Jonathan Wells - May 2012
Excerpt: Evidence shows that non-DNA developmental information can be inherited in several ways. For example, it can be inherited through chromatin modifications, which affect gene expression without altering underlying DNA sequences. Another example is cytoplasmic inheritance, which involves cytoskeletal patterns and localization of intracellular molecules. Still another example is cortical inheritance, which involves membrane patterns.

“Live memory” of the cell, the other hereditary memory of living systems - 2005
Excerpt: To understand this notion of “live memory”, its role and interactions with DNA must be resituated; indeed, operational information belongs as much to the cell body and to its cytoplasmic regulatory protein components and other endogenous or exogenous ligands as it does to the DNA database. We will see in Section 2, using examples from recent experiments in biology, the principal roles of “live memory” in relation to the four aspects of cellular identity, memory of form, hereditary transmission and also working memory.

Cortical Inheritance: The Crushing Critique Against Genetic Reductionism - Arthur Jones - video

New Insights Into How (Adult) Stem Cells Determine What Tissue to Become - August 2010
Excerpt: Within 24 hours of culturing adult human stem cells on a new type of matrix, University of Michigan researchers were able to make predictions about how the cells would differentiate, or what type of tissue they would become.,,, "Our research confirms that mechanical factors are as important as the chemical factors regulating differentiation," Fu said. "The mechanical aspects have, until now, been largely ignored by stem cell biologists."

An Electric Face: A Rendering Worth a Thousand Falsifications - September 2011
Excerpt: The video suggests that bioelectric signals presage the morphological development of the face. It also, in an instant, gives a peak at the phenomenal processes at work in biology. As the lead researcher said, “It’s a jaw dropper.”

The (Electric) Face of a Frog - video

Scientists' 3-D View of Genes-at-Work Is Paradigm Shift in Genetics - Dec. 2009
Excerpt: Highly coordinated chromosomal choreography leads genes and the sequences controlling them, which are often positioned huge distances apart on chromosomes, to these 'hot spots'. Once close together within the same transcription factory, genes get switched on (a process called transcription) at an appropriate level at the right time in a specific cell type. This is the first demonstration that genes encoding proteins with related physiological role visit the same factory.

3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell - Oct. 2009
Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip -- while avoiding the knots and tangles that might interfere with the cell's ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication.

Moreover, another '4-Dimensional' aspect of life, besides changing with time as Dr. Carter pointed out in the video, is that biological life actually does scale directly to 4-Dimensional parameters instead of scaling to 3-Dimensional parameters as would be expected from the materialistic theory of neo-Darwinism:

The predominance of quarter-power (4-D) scaling in biology
Excerpt: Many fundamental characteristics of organisms scale
with body size as power laws of the form:

Y = Yo M^b,

where Y is some characteristic such as metabolic rate, stride length or life span, Yo is a normalization constant, M is body mass and b is the allometric scaling exponent.
A longstanding puzzle in biology is why the exponent b is usually some simple multiple of 1/4 (4-Dimensional scaling) rather than a multiple of 1/3, as would be expected from Euclidean (3-Dimensional) scaling.

“Although living things occupy a three-dimensional space, their internal physiology and anatomy operate as if they were four-dimensional. Quarter-power scaling laws are perhaps as universal and as uniquely biological as the biochemical pathways of metabolism, the structure and function of the genetic code and the process of natural selection.,,, The conclusion here is inescapable, that the driving force for these invariant scaling laws cannot have been natural selection." Jerry Fodor and Massimo Piatelli-Palmarini, What Darwin Got Wrong (London: Profile Books, 2010), p. 78-79

4-Dimensional Quarter Power Scaling In Biology - video

Though Jerry Fodor and Massimo Piatelli-Palmarini rightly find it inexplicable for 'random' Natural Selection to be the rational explanation for the invariant scaling of the physiology, and anatomy, of living things to four-dimensional parameters, they do not seem to fully realize the implications this 'four dimensional scaling' of living things presents. This 4-D scaling is something we should rightly expect from a Intelligent Design perspective. This is because Intelligent Design holds that ‘higher dimensional transcendent information’ is more foundational to life, and even to the universe itself, than either matter or energy are. This higher dimensional 'expectation' for life, from a Intelligent Design perspective, is directly opposed to the expectation of the Darwinian framework, which holds that information, and indeed even the essence of life itself, is merely an 'emergent' property of the 3-D material realm.

Information and entropy – top-down or bottom-up development in living systems? A.C. McINTOSH
Excerpt: This paper highlights the distinctive and non-material nature of information and its relationship with matter, energy and natural forces. It is proposed in conclusion that it is the non-material information (transcendent to the matter and energy) that is actually itself constraining the local thermodynamics to be in ordered disequilibrium and with specified raised free energy levels necessary for the molecular and cellular machinery to operate.

Multidimensional Genome, DNA Architecture, Genes, Genome Organization, Robert Carter, John Sanford, Intelligent Design, Jesus Is Lord
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